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Hi, first of all, thanks for this fantastic tool.
I am working on my CosMX data and I can't find a way to save the Workspace nor the Giotto object in RDS. I think the polygon data is not be…
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Hi team,
Thanks for the great package and all the useful tutorials for different types of spatial data!
I have been following the manual for the CosMx data and faced some errors/issues, leading to …
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Please add the following
```r
# Handle older assay probe labels
if (pkcData[["RTS_ID"]][1] %like% "^RTS" &
probeAssay[["RTS_ID"]][1] %like% "^RNA") {
# replace RTS00 with RNA in pro…
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Right now file and software version are taken from the DCC, but are reversioned with numeric_version and does not match the DCC file. If the intent was to have a tracking system to match DCC this shou…
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Where is the "metadata_giotto.csv" in data_preparation.ipynb in nanostring_cosmx_human_nsclc dataset?
I can't find "metadata_giotto.csv" in https://nanostring.com/products/cosmx-spatial-molecular-ima…
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Idea: can we use cells' neighborhoods to estimate the background they're getting from segmentation errors?
step 1: use each cell's neighbors to estimate the 'background' from segmentation errors th…
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## Please use the template below to post a question to https://discourse.scverse.org/c/ecosytem/cell2location/.
### Problem
when running this code : from cell2location.plt import plot_spatial
…
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Hi,
Thank you for introducing the "napari-cosmx plugin" in the Nanostring Blog.
Following the steps outlined in the blog, I successfully created a napari-ready slide file from AtoMx raw data usi…
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**User story**
Annotations like ROI's are often present in OME-TIFF files and can be rendered as overlays on an image. Furthermore, users may want to add annotations to an image on their screen. Vi…
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## Please use the template below to post a question to https://discourse.scverse.org/c/ecosytem/cell2location/.
### Problem
I would like to estimate the proportion of cell types in each spot.…